1. When writing a fiction how do you decide gender? Is it ever symbolic, is it random, or is it whatever yours is?

I think making gender symbolic in your standard, every day, non-philosophical fic is a mite pretentious (without good reason, of course). As far as I'm concerned, gender's a completely random, natural phenomenon. What you need to worry about is gender-balance and the characterization of genders.

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2. What about side characters? Is there always a certain amount of characters of a certain gender or do you also make this random?

Whatever works, really. I like to have a good distribution of genders, but it usually comes naturally. I don't plan out the gender of every minor character and what that might symbolize.

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Finally my question: How would one go about keeping gender anonymous? I don't want to tell the exact gender of the main character.

Basically what Bobandbill said. But if you really have to go for a 3rd person POV, try not to be preferential towards a single pronoun. It's actually quite hard, imo, to have a 3rd person protagonist of unknown gender, that's also not one-dimensional. People are usually characterized by internalized gender norms, so they tend to act like one gender or the other. It's all fine and well to keep gender under wraps, but eventually their mannerisms could betray the secret. Your best bet, I think, is to flat-out reference the ambiguity in the beginning and continue with either a preferentially masculine/feminine character. The latter mostly to make the main character seem human, I suppose. It does wonders for likeability. Acting like you don't have a gender makes you seem like a one-dimensional robot, barring of course Asimovian examples, but even then the more developed of Asimov's robots tend to gravitate towards a specific gender norm.